Genome-wide identification of HD-ZIP transcription factors in maize and their regulatory roles in promoting drought tolerance

Functional study of ZmHDZ4 in maize (Zea mays) seedlings under drought stress

BACKGROUND

Maize is a major feed and industrial crop and pivotal for ensuring global food security. In light of global warming and climate change, improving maize tolerance to water deficit is crucial. Identification and functional analysis of drought tolerance genes have potential practical importance in understanding the molecular mechanisms of drought stress.

RESULTS

Here, we identified a maize Homeodomain-Leucine Zipper I, ZmHDZ4, in maize seedlings that is associated with drought tolerance. We demonstrated that ZmHDZ4 has transcriptional activation activity, exclusively localized in the nucleus. Several Cis-acting elements associated with abiotic stress have been identified in the core promoter region of ZmHDZ4. Under drought-stressed conditions, transgenic maize plants overexpressing ZmHDZ4 exhibited significantly higher relative water content and peroxidase (POD) and superoxidase dismutase (SOD) activities compared to wide-type plants, while displaying lower malondialdehyde (MAD) content. The expressions of ZmMFS1-88, ZmGPM573, and ZmPHD9 were significantly repressed in the ZmHDZ4-OE plants under drought-stressed conditions, indicating that ZmMFS1-88, ZmGPM573, and ZmPHD9 were the candidate target genes of ZmHDZ4.

CONCLUSIONS

ZmHDZ4 is involved in the regulation of drought stress tolerance in maize by participating in osmotic regulation, sugar metabolism pathways, and hormone regulation.

ZmABF4-ZmVIL2/ZmFIP37 module enhances drought tolerance in maize seedlings

Drought, as a primary environmental factor, imposes significant constraints on developmental processes and productivity of plants. PHDs were identified as stress-responsive genes in a wide range of eukaryotes. However, the regulatory mechanisms governing PHD genes in maize under abiotic stress conditions are still largely unknown and require further investigation. Here, we identified a mutant, zmvil2, in the EMS mutant library with a C to T mutation in the exon of the Zm00001d053875 (VIN3-like protein 2, ZmVIL2), resulting in premature termination of protein coding. ZmVIL2 belongs to PHD protein family. Compared to WT, zmvil2 mutant exhibited increased sensitivity to drought stress. Consistently, overexpression of ZmVIL2 enhances drought resistance in maize. Y2H, BiFC, and Co-IP experiments revealed that ZmVIL2 directly interacts with ZmFIP37 (FKBP12-interacting protein of 37). zmfip37 knockout mutants also exhibit decreased drought tolerance. Interestingly, we demonstrated that ZmABF4 directly binds to the ZmVIL2 promoter to enhance its activity in yeast one hybrid (Y1H), electrophoretic mobility shift assay (EMSA) and dual luciferase reporter assays. Therefore, we uncovered a novel model ZmABF4-ZmVIL2/ZmFIP37 that promotes drought tolerance in maize. Overall, these findings have enriched the knowledge of the functions of PHD genes in maize and provides genetic resources for breeding stress-tolerant maize varieties.

Passion fruit HD-ZIP genes: Characterization, expression variance, and overexpression PeHB31 enhanced drought tolerance via lignin pathway

The HD-ZIP (homeodomain-leucine zipper) genes hold significant importance in transcriptional regulation, especially in plant development and responses to abiotic stresses. However, a comprehensive study targeting HD-ZIP family members in passion fruit has been absent. In our current research, 34 HD-ZIP family members (PeHBs) were identified by bioinformatics analysis. Transcriptome analysis revealed that PeHBs exhibited distinct expression patterns when subjected to the four different abiotic stresses, and significant differential expression of PeHBs was also found among the three developmental stages of the fruit and between the purple and yellow genotype passion fruit leaves. An integrated metabolome and transcriptome analysis further revealed that the HD-ZIP III class gene PeHB31 (homologous to ATHB8), was co-upexpressed with lignans in yellow fruit P. edulis (commonly used as a resistance rootstock) when compared to purple fruit P. edulis. The transformation of Arabidopsis and yeast with the PeHB31 gene showed an enhancement in their capacity to withstand drought conditions. Notably, the transgenic Arabidopsis plants exhibited an increase in lignin content within the vascular tissues of their stems. This research lays the groundwork for future studies on the control mechanisms of lignin biosynthesis by HD-ZIP genes (especially HD-ZIP classes III and I) involved in drought tolerance.

Genetic, molecular and physiological crosstalk during drought tolerance in maize (Zea mays): pathways to resilient agriculture

MAIN CONCLUSION

This review comprehensively elucidates maize drought tolerance mechanisms, vital for global food security. It highlights genetic networks, key genes, CRISPR-Cas applications, and physiological responses, guiding resilient variety development. Maize, a globally significant crop, confronts the pervasive challenge of drought stress, impacting its growth and yield significantly. Drought, an important abiotic stress, triggers a spectrum of alterations encompassing maize's morphological, biochemical, and physiological dimensions. Unraveling and understanding these mechanisms assumes paramount importance for ensuring global food security. Approaches like developing drought-tolerant varieties and harnessing genomic and molecular applications emerge as effective measures to mitigate the negative effects of drought. The multifaceted nature of drought tolerance in maize has been unfolded through complex genetic networks. Additionally, quantitative trait loci mapping and genome-wide association studies pinpoint key genes associated with drought tolerance, influencing morphophysiological traits and yield. Furthermore, transcription factors like ZmHsf28, ZmNAC20, and ZmNF-YA1 play pivotal roles in drought response through hormone signaling, stomatal regulation, and gene expression. Genes, such as ZmSAG39, ZmRAFS, and ZmBSK1, have been reported to be pivotal in enhancing drought tolerance through diverse mechanisms. Integration of CRISPR-Cas9 technology, targeting genes like gl2 and ZmHDT103, emerges as crucial for precise genetic enhancement, highlighting its role in safeguarding global food security amid pervasive drought challenges. Thus, decoding the genetic and molecular underpinnings of drought tolerance in maize sheds light on its resilience and paves the way for cultivating robust and climate-smart varieties, thus safeguarding global food security amid climate challenges. This comprehensive review covers quantitative trait loci mapping, genome-wide association studies, key genes and functions, CRISPR-Cas applications, transcription factors, physiological responses, signaling pathways, offering a nuanced understanding of intricate mechanisms involved in maize drought tolerance.

Regulatory mechanisms used by ZmMYB39 to enhance drought tolerance in maize (Zea mays) seedlings

Drought is a significant abiotic stressor that limits maize (Zea mays L.) growth and development. Thus, enhancing drought tolerance is critical for promoting maize production. Our findings demonstrated that ZmMYB39 is an MYB transcription factor with transcriptional activation activity. Drought stress experiments involving ZmMYB39 overexpression and knockout lines indicated that ZmMYB39 positively regulated drought stress tolerance in maize. DAP-Seq, EMSA, dual-LUC, and RT-qPCR provided initial insights into the molecular regulatory mechanisms by which ZmMYB39 enhances drought tolerance in maize. ZmMYB39 directly promoted the expression of ZmP5CS1, ZmPOX1, ZmSOD2, ZmRD22, ZmNAC49, and ZmDREB2A, which are involved in stress resistance. ZmMYB39 enhanced drought tolerance by interacting with and promoting the expression of ZmFNR1, ZmHSP20, and ZmDOF6. Our study offers a theoretical basis for understanding the molecular regulatory networks involved in maize drought stress response. Furthermore, ZmMYB39 serves as a valuable genetic resource for breeding drought-resistant maize.

Seedling root system adaptation to water availability during maize domestication and global expansion

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.

Mechanism of action of microRNA166 on nitric oxide in alfalfa (Medicago sativa L.) under drought stress

BACKGROUND

Alfalfa is a perennial forage crop of high importance, but its cultivation is often affected by drought stress. Currently, the investigation of drought-related small RNAs is a popular research topic to uncover plant drought resistance mechanisms. Among these small RNAs, microRNA166 (miR166) is associated with drought in numerous plant species. Initial small RNA sequencing studies have shown that miR166 is highly responsive to exogenous nitric oxide (NO) and drought. Therefore, analyzing the expression of Msa-miR166 under nitric oxide and drought treatment is significant.

RESULT

Bioinformatics analysis revealed that the miR166 family is widely distributed among plants, ranging from mosses to eudicots, with significant distribution differences between species. The evolutionary degree of Msa-miR166s is highly similar to that of Barrel medic (Medicago truncatula) and Soybean (Glycine max), but significantly different from the model plant Arabidopsis (Arabidopsis thaliana). It is suggested that there are no significant differences in miR166s within the species, and members of Msa-miR166s can form a typical stem-loop. The lowest level of exogenous nitric oxide was observed in Msa-miR166s under drought stress, followed by individual drought, and the highest level was observed after removing endogenous nitric oxide.

CONCLUSION

In response to short-term drought, Msa-miR166s down-regulate expression in alfalfa (Medicago sativa L.). Exogenous nitric oxide can reduce the expression of Msa-miR166s in response to short-term drought. These findings suggest that Msa-miR166e-5p is responsive to environmental changes. The expression levels of target genes showed an opposite trend to Msa-miR166s, verifying the accuracy of Degradome sequencing in the early stage. This suggests that alfalfa experiences drought stress when regulated by exogenous nitric oxide, targeting HD ZIP-III, FRI, and CoA ligase genes. Additionally, the expression of Msa-miR166s in response to drought stress varies between leaves and roots, indicating spatiotemporal specificity.

ZmC2H2-149 negatively regulates drought tolerance by repressing ZmHSD1 in maize

Drought is a major abiotic stress that limits maize production worldwide. Therefore, it is of great importance to improve drought tolerance in crop plants for sustainable agriculture. In this study, we examined the roles of Cys2 /His2 zinc-finger-proteins (C2H2-ZFPs) in maize's drought tolerance as C2H2-ZFPs have been implicated for plant stress tolerance. By subjecting 150 Ac/Ds mutant lines to drought stress, we successfully identified a Ds-insertion mutant, zmc2h2-149, which shows increased tolerance to drought stress. Overexpression of ZmC2H2-149 in maize led to a decrease in both drought tolerance and crop yield. DAP-Seq, RNA-Seq, Y1H and LUC assays additionally showed that ZmC2H2-149 directly suppresses the expression of a positive drought tolerance regulator, ZmHSD1 (hydroxysteroid dehydrogenase 1). Consistently, the zmhsd1 mutants exhibited decreased drought tolerance and grain yield under water deficit conditions compared to their respective wild-type plants. Our findings thus demonstrated that ZmC2H2-149 can regulate ZmHSD1 for drought stress tolerance in maize, offering valuable theoretical and genetic resources for maize breeding programmes that aim for improving drought tolerance.

Analysis of the molecular mechanisms regulating how ZmEREB24 improves drought tolerance in maize (Zea mays) seedlings

Drought stress is one of the most limiting factors of maize productivity and can lead to a sharp reduction in the total biomass when it occurs at the seedling stage. Improving drought tolerance at the seedling stage is of great importance for maize breeding. The AP2/ERF transcription factor family plays a critical role in plant response to abiotic stresses. Here, we used a preliminary previously-generated ranscriptomic dataset to identify a highly drought-stress-responsive AP2 gene, i.e., ZmEREB24. Compared to the wild type, the overexpression of ZmEREB24 in maize significantly promotes drought tolerance of transgenic plants at the seedling stage. CRISPR/Cas9-based ZmEREB24-knockout mutants showed a drought-sensitive phenotype. RNA-seq analysis and EMSA assay revealed AATGG.CT and GTG.T.GCC motifs as the main binding sites of ZmEREB24 to the promoters of downstream target genes. DAP-seq identified four novel target genes involved in proline and sugar metabolism and hormone signal transduction of ZmEREB24. Our data indicate that ZmEREB24 plays important biological functions in regulating drought tolerance by binding to the promoters of drought stress genes and modulating their expression. The results further suggest a role of ZmEREB24 in regulating drought adaptation in maize, indicating its potential importance for employing molecular breeding in the development of high-yield drought-tolerant maize cultivars.

Photosynthesis Response and Transcriptional Analysis: Dissecting the Role of SlHB8 in Regulating Drought Resistance in Tomato Plants

Deciphering drought resistance in crops is crucial for enhancing water productivity. Previous studies have highlighted the significant role of the transcription factor SlHB8 in regulating developmental processes in tomato plants but its involvement in drought resistance remains unclear. Here, gene overexpression (SlHB8-OE) and gene knockout (slhb8) tomato plants were utilized to study the role of SlHB8 in regulating drought resistance. Our findings showed that slhb8 plants exhibited a robust resistant phenotype under drought stress conditions. The stomata of slhb8 tomato leaves displayed significant closure, effectively mitigating the adverse effects of drought stress on photosynthetic efficiency. The slhb8 plants exhibited a decrease in oxidative damage and a substantial increase in antioxidant enzyme activity. Moreover, slhb8 effectively alleviated the degree of photoinhibition and chloroplast damage caused by drought stress. SlHB8 regulates the expression of numerous genes related to photosynthesis (such as SlPSAN, SlPSAL, SlPSBP, and SlTIC62) and stress signal transduction (such as SlCIPK25, SlABA4, and SlJA2) in response to drought stress. Additionally, slhb8 plants exhibited enhanced water absorption capacity and upregulated expression of several aquaporin genes including SlPIP1;3, SlPIP2;6, SlTIP3;1, SlNIP1;2, and SlXIP1;1. Collectively, our findings suggest that SlHB8 plays a negative regulatory role in the drought resistance of tomato plants.

Comparative analysis of tissue-specific genes in maize based on machine learning models: CNN performs technically best, LightGBM performs biologically soundest

Introduction: With the advancement of RNA-seq technology and machine learning, training large-scale RNA-seq data from databases with machine learning models can generally identify genes with important regulatory roles that were previously missed by standard linear analytic methodologies. Finding tissue-specific genes could improve our comprehension of the relationship between tissues and genes. However, few machine learning models for transcriptome data have been deployed and compared to identify tissue-specific genes, particularly for plants. Methods: In this study, an expression matrix was processed with linear models (Limma), machine learning models (LightGBM), and deep learning models (CNN) with information gain and the SHAP strategy based on 1,548 maize multi-tissue RNA-seq data obtained from a public database to identify tissue-specific genes. In terms of validation, V-measure values were computed based on k-means clustering of the gene sets to evaluate their technical complementarity. Furthermore, GO analysis and literature retrieval were used to validate the functions and research status of these genes. Results: Based on clustering validation, the convolutional neural network outperformed others with higher V-measure values as 0.647, indicating that its gene set could cover as many specific properties of various tissues as possible, whereas LightGBM discovered key transcription factors. The combination of three gene sets produced 78 core tissue-specific genes that had previously been shown in the literature to be biologically significant. Discussion: Different tissue-specific gene sets were identified due to the distinct interpretation strategy for machine learning models and researchers may use multiple methodologies and strategies for tissue-specific gene sets based on their goals, types of data, and computational resources. This study provided comparative insight for large-scale data mining of transcriptome datasets, shedding light on resolving high dimensions and bias difficulties in bioinformatics data processing.

Functional analysis of a late embryogenesis abundant protein ZmNHL1 in maize under drought stress

Maize is an important feed and industrial cereal crop and is crucial for global food security. The development of drought-tolerant genotypes is a major aim of breeding programs to fight water scarcity and maintain sustainable maize production. Late embryogenesis abundant (LEA) proteins are a family of proteins related to osmotic regulation that widely exist in organisms. Here, we implemented a previously generated maize transcriptomic dataset to identify a drought-responsive gene designated ZmNHL1. Bioinformatics analysis of ZmNHL1 showed that the protein encoded by ZmNHL1 belongs to the LEA-2 protein family. Tissue specific expression analysis showed that ZmNHL1 is relatively abundant in stems and leaves, highly expressed in tassels and only slightly expressed in roots, pollens and ears. Moreover, the activity of SOD and POD of plants from three 35S::ZmNHL1 transgenic lines under either the induced drought stress conditions (by 20% PEG6000) or the natural water deficit treatment (by water withholding) were higher than that of the WT plants, while the electrolyte leakage of the 35S::ZmNHL1 transgenic plants was lower than that of the WT plants under both drought treatments. Our data further revealed that ZmNHL1 promotes maize tolerance to drought stress in 35S::ZmNHL1 transgenic plants by improving ROS scavenging and maintaining the cell membrane permeability. Overall, our data revealed that ZmNHL1 promotes maize tolerance to drought stress and contributes to provide elite germplasm resources for maize drought tolerance breeding programs.

Identification and Functional Characterization of the RcFAH12 Promoter from Castor Bean in Arabidopsis thaliana

Castor (Ricinus communis L.) seed oil is the commercial source of ricinoleate, a valuable raw material used in many industries. Oleoyl-12-hydroxylase (RcFAH12) is a key enzyme in the biosynthesis of ricinoleate, accumulating nearly 90% of the triacylglycerol in castor seeds. Little is known about the transcriptional regulation of RcFAH12. We used rapid amplification of cDNA 5′ ends (5′RACE) to locate the transcription start site (TSS) of RcFAH12, and the sequence of a 2605 bp region, −2506~+99, surrounding the TSS was cloned. We then investigated these regions to promote β-glucuronidase (GUS) expression in transgenic Arabidopsis by the progressive 5′ and 3′ deletions strategies. The GUS staining showed that the GUS accumulation varied in tissues under the control of different deleted fragments of RcFAH12. In addition, the GUS expression driven by the RcFAH12 promoter markedly accumulated in transgenic seeds, which indicated that RcFAH12 might play an important role in the biosynthesis of ricinoleic acid. This study will lay a potential foundation for developing a tissue-specific promoter in oil-seed crops.

Identification and Characterization of the HD-Zip Gene Family and Dimerization Analysis of HB7 and HB12 in Brassica napus L

Homeodomain-leucine zipper (HD-Zip) genes encode plant-specific transcription factors, which play important roles in plant growth, development, and response to environmental stress. These genes have not been fully studied in allopolyploid Brassica napus, an important kind of oil crop. In this study, 165 HD-Zip genes were identified in B. napus and classified into four subfamilies. If proteins belong to the same subfamily, they exhibit similarities in gene structure, motifs, and domain distribution patterns. BnHD-Zip genes were unevenly distributed in the An and Cn subgenomes. Whole genome triplication (WGT) events may be major mechanisms accounting for this gene family expansion. Orthologous gene analysis showed that the process of this gene family expansion was accompanied by domain loss. We further found three genes homologous to HB7 and three genes homologous to HB12, all induced by PEG, ABA, and NaCl treatment. HB7 could not form homodimers but could form heterodimers with HB12 based on yeast two-hybrid assays. The results of this study provide valuable information for further exploration of the HD-Zip gene family in B. napus.

The roles of HD-ZIP proteins in plant abiotic stress tolerance

Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.